Theory of Bubble Nucleation and Cooperativity in DNA Melting

The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles and the possibility of a two states transition are studied.Comment: 4 figures. Accepted for publication in Physical Review Letter

Non Local Electron-Phonon Correlations in a Dispersive Holstein Model

Due to the dispersion of optical phonons, long range electron-phonon correlations renormalize downwards the coupling strength in the Holstein model. We evaluate the size of this effect both in a linear chain and in a square lattice for a time averaged {\it e-ph} potential, where the time variable is introduced according to the Matsubara formalism. Mapping the Holstein Hamiltonian onto the time scale we derive the perturbing source current which appears to be non time retarded. This property permits to disentangle phonon and electron coordinates in the general path integral for an electron coupled to dispersive phonons. While the phonon paths can be integrated out analytically, the electron path integrations have to be done numerically. The equilibrium thermodynamic properties of the model are thus obtained as a function of the electron hopping value and of the phonon spectrum parameters. We derive the {\it e-ph} corrections to the phonon free energy and show that its temperature derivatives do not depend on the {\it e-ph} effective coupling hence, the Holstein phonon heat capacity is strictly harmonic. A significant upturn in the low temperature total heat capacity over $T$ ratio is attributed to the electron hopping which largely contributes to the action.Comment: Phys.Rev.B (2005

Probing the mechanical unzipping of DNA

A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on unzipping speed and temperature. Our findings agree quantitatively with experimental results for homogeneous DNA, and for $\lambda$-phage DNA we reproduce the recently obtained experimental force-temperature phase diagram. Finally, we argue that there may be fundamental differences between {\em in vivo} and {\em in vitro} DNA unzipping

Path Integral of the Holstein Model with a ϕ4\phi^4 on site potential

We derive the path integral of the semiclassical, one dimensional anharmonic Holstein model assuming that the electron motion takes place in a bath of non linear oscillators with quartic on site hard (and soft) potentials. The interplay between {\it e-ph} coupling and anharmonic force constant is analysed both in the adiabatic and antiadiabatic regime. In the latter we find much larger anharmonic features on the thermodynamic properties of low energy oscillators. Soft on site potentials generate attractive centres at large amplitude oscillator paths and contribute to the anomalous shape of the {\it heat capacity over temperature} ratio in the intermediate to low $T$ range. This anharmonic lattice effect is superimposed to the purely electronic contribution associated to a temperature dependent hopping with variable range inducing local disorder in the system.Comment: To be published in Phys.Rev.

Regional and global temperature response to anthropogenic SO2 emissions from China in three climate models

We use the HadGEM3-GA4, CESM1, and GISS ModelE2 climate models to investigate the global and regional aerosol burden, radiative flux, and surface temperature responses to removing anthropogenic sulfur dioxide (SO2) emissions from China. We find that the models differ by up to a factor of six in the simulated change in aerosol optical depth (AOD) and shortwave radiative flux over China that results from reduced sulfate aerosol, leading to a large range of magnitudes in the regional and global temperature responses. Two of the three models simulate a near-ubiquitous hemispheric warming due to the regional SO2 removal, with similarities in the local and remote pattern of response, but overall with a substantially different magnitude. The third model simulates almost no significant temperature response. We attribute the discrepancies in the response to a combination of substantial differences in the chemical conversion of SO2 to sulfate, translation of sulfate mass into AOD, cloud radiative interactions, and differences in the radiative forcing efficiency of sulfate aerosol in the models. The model with the strongest response (HadGEM3-GA4) compares best with observations of AOD regionally, however the other two models compare similarly (albeit poorly) and still disagree substantially in their simulated climate response, indicating th at total AOD observations are far from sufficient to determine which model response is more plausible. Our results highlight that there remains a large uncertainty in the representation of both aerosol chemistry as well as direct and indirect aerosol radiative effects in current climate models, and reinforces that caution must be applied when interpreting the results of modelling studies of aerosol influences on climate. Model studies that implicate aerosols in climate responses should ideally explore a range of radiative forcing strengths representative of this uncertainty, in addition to thoroughly evaluating the models used against observations

Global Multi-Year O3-CO Correlation Patterns from Models and TES Satellite Observations

The correlation between measured tropospheric ozone (O3) and carbon monoxide (CO) has been used extensively in tropospheric chemistry studies to explore the photochemical characteristics of different regions and to evaluate the ability of models to capture these characteristics. Here, we present the first study that uses multi-year, global, vertically resolved, simultaneous and collocated O3 and CO satellite (Tropospheric Emission Spectrometer) measurements, to determine this correlation in the middle/lower free troposphere for two different seasons, and to evaluate two chemistry-climate models. We find results that are fairly robust across different years, altitudes and timescales considered, which indicates that the correlation maps presented here could be used in future model evaluations. The highest positive correlations (around 0.8) are found in the northern Pacific during summer, which is a common feature in the observations and the G-PUCCINI model. We make quantitative comparisons between the models using a single-figure metric (C), which we define as the correlation coefficient between the modeled and the observed O3-CO correlations for different regions of the globe. On a global scale, the G-PUCCINI model shows a good performance in the summer (C =0.71) and a satisfactory performance in the winter (C = 0.52). It captures midlatitude features very well, especially in the summer, whereas the performance in regions like South America or Central Africa is weaker. The UKCA model (C = 0.46/0.15 for July-August/December-January on a global scale) performs better in certain regions, such as the tropics in winter, and it captures some of the broad characteristics of summer extratropical correlations, but it systematically underestimates the O3-CO correlations over much of the globe. It is noteworthy that the correlations look very different in the two models, even though the ozone distributions are similar. This demonstrates that this technique provides a powerful global constraint for understanding modeled tropospheric chemical processes. We investigated the sources of the correlations by performing a series of sensitivity experiments. In these, the sign of the correlation is, in most cases, insensitive to removing different individual emissions, but its magnitude changes downwind of emission regions when applying such perturbations. Interestingly, we find that the O3-CO correlation does not solely reflect the strength of O3 photochemical production, as often assumed by earlier studies, but is more complicated and may reflect a mixture of different processes such as transport

Particle Path Correlations in a Phonon Bath

The path integral formalism is applied to derive the full partition function of a generalized Su-Schrieffer-Heeger Hamiltonian describing a particle motion in a bath of oscillators. The electronic correlations are computed versus temperature for some choices of oscillators energies. We study the perturbing effect of a time averaged particle path on the phonon subsystem deriving the relevant temperature dependent cumulant corrections to the harmonic partition function and free energy. The method has been applied to compute the total heat capacity up to room temeperature: a low temperature upturn in the heat capacity over temperature ratio points to a glassy like behavior ascribable to a time dependent electronic hopping with variable range in the linear chain.Comment: To be published in J.Phys.:Condensed Matte

Understanding the glacial methane cycle.

Atmospheric methane (CH4) varied with climate during the Quaternary, rising from a concentration of 375 p.p.b.v. during the last glacial maximum (LGM) 21,000 years ago, to 680 p.p.b.v. at the beginning of the industrial revolution. However, the causes of this increase remain unclear; proposed hypotheses rely on fluctuations in either the magnitude of CH4 sources or CH4 atmospheric lifetime, or both. Here we use an Earth System model to provide a comprehensive assessment of these competing hypotheses, including estimates of uncertainty. We show that in this model, the global LGM CH4 source was reduced by 28-46%, and the lifetime increased by 2-8%, with a best-estimate LGM CH4 concentration of 463-480 p.p.b.v. Simulating the observed LGM concentration requires a 46-49% reduction in sources, indicating that we cannot reconcile the observed amplitude. This highlights the need for better understanding of the effects of low CO2 and cooler climate on wetlands and other natural CH4 sources

The global methane budget 2000-2017

Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. Atmospheric emissions and concentrations of CH4 continue to increase, making CH4 the second most important human-influenced greenhouse gas in terms of climate forcing, after carbon dioxide (CO2). The relative importance of CH4 compared to CO2 depends on its shorter atmospheric lifetime, stronger warming potential, and variations in atmospheric growth rate over the past decade, the causes of which are still debated. Two major challenges in reducing uncertainties in the atmospheric growth rate arise from the variety of geographically overlapping CH4 sources and from the destruction of CH4 by short-lived hydroxyl radicals (OH). To address these challenges, we have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate new research aimed at improving and regularly updating the global methane budget. Following Saunois et al. (2016), we present here the second version of the living review paper dedicated to the decadal methane budget, integrating results of top-down studies (atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up estimates (including process-based models for estimating land surface emissions and atmospheric chemistry, inventories of anthropogenic emissions, and data-driven extrapolations). For the 2008-2017 decade, global methane emissions are estimated by atmospheric inversions (a top-down approach) to be 576 Tg CH4 yr-1 (range 550-594, corresponding to the minimum and maximum estimates of the model ensemble). Of this total, 359 Tg CH4 yr-1 or ĝ1/4 60 % is attributed to anthropogenic sources, that is emissions caused by direct human activity (i.e. anthropogenic emissions; range 336-376 Tg CH4 yr-1 or 50 %-65 %). The mean annual total emission for the new decade (2008-2017) is 29 Tg CH4 yr-1 larger than our estimate for the previous decade (2000-2009), and 24 Tg CH4 yr-1 larger than the one reported in the previous budget for 2003-2012 (Saunois et al., 2016). Since 2012, global CH4 emissions have been tracking the warmest scenarios assessed by the Intergovernmental Panel on Climate Change. Bottom-up methods suggest almost 30 % larger global emissions (737 Tg CH4 yr-1, range 594-881) than top-down inversion methods. Indeed, bottom-up estimates for natural sources such as natural wetlands, other inland water systems, and geological sources are higher than top-down estimates. The atmospheric constraints on the top-down budget suggest that at least some of these bottom-up emissions are overestimated. The latitudinal distribution of atmospheric observation-based emissions indicates a predominance of tropical emissions (ĝ1/4 65 % of the global budget, < 30ĝ  N) compared to mid-latitudes (ĝ1/4 30 %, 30-60ĝ  N) and high northern latitudes (ĝ1/4 4 %, 60-90ĝ  N). The most important source of uncertainty in the methane budget is attributable to natural emissions, especially those from wetlands and other inland waters. Some of our global source estimates are smaller than those in previously published budgets (Saunois et al., 2016; Kirschke et al., 2013). In particular wetland emissions are about 35 Tg CH4 yr-1 lower due to improved partition wetlands and other inland waters. Emissions from geological sources and wild animals are also found to be smaller by 7 Tg CH4 yr-1 by 8 Tg CH4 yr-1, respectively. However, the overall discrepancy between bottom-up and top-down estimates has been reduced by only 5 % compared to Saunois et al. (2016), due to a higher estimate of emissions from inland waters, highlighting the need for more detailed research on emissions factors. Priorities for improving the methane budget include (i) a global, high-resolution map of water-saturated soils and inundated areas emitting methane based on a robust classification of different types of emitting habitats; (ii) further development of process-based models for inland-water emissions; (iii) intensification of methane observations at local scales (e.g., FLUXNET-CH4 measurements) and urban-scale monitoring to constrain bottom-up land surface models, and at regional scales (surface networks and satellites) to constrain atmospheric inversions; (iv) improvements of transport models and the representation of photochemical sinks in top-down inversions; and (v) development of a 3D variational inversion system using isotopic and/or co-emitted species such as ethane to improve source partitioning. The data presented here can be downloaded from https://doi.org/10.18160/GCP-CH4-2019 (Saunois et al., 2020) and from the Global Carbon Project